Ideas for an overview manuscript

ondrejkrejci commented 1 year ago

[x] Journal Ideas
[ ] List of tasks to be completed and to be mentioned in the manuscript:
- [x] working on PiP (#55) and all platforms (#27 ):
- [x] working damping (#48) and parameters for Pauli (full density)
- [x] KPFM
- [ ] GUI (#42)
- [x] GPU version (#35)

To be closed after the paper has been accepted.

ondrejkrejci commented 8 months ago

[x] #259
[x] #260
[x] #261 should be part of the documentation.

ondrejkrejci commented 8 months ago

I have added the arXiv manuscript citation to our wiki. Should we add it to our readme, or do we wait, until is it published?

NikoOinonen commented 8 months ago

We probably should add a whole section about citing the code and the paper, but probably after it's published, I think.

ProkopHapala commented 8 months ago

I think both is good. If you whant to put the arXiv there now, why not. If you have time now, and you feel like you want to do it, it is definitely good to update the wiki and README.md.

mondracek commented 7 months ago

Do not forget to correct A=1.2 to A=12 in the caption under Figure 2 once the paper is in the proof stage.

ProkopHapala commented 7 months ago

Hi @ondrejkrejci and others, any news about the manuscript? (to be honest I expected it will be acceptate rather quickly and smoothly)

yakutovicha commented 7 months ago

Hi @ondrejkrejci and others, any news about the manuscript? (to be honest I expected it will be acceptate rather quickly and smoothly)

We all should have received an email with the tracking link.

ondrejkrejci commented 7 months ago

@ProkopHapala - unfortunately no response so far. I am checking my junk email pretty often these days. I cannot blame anyone now. I had a month delay for one review in Jauary ...

ProkopHapala commented 4 months ago

Hi, @ondrejkrejci - I did significant modification to your updates of the manuscript text, but I kept your version in comment %.

Ad bio-AFM-simulation references - I would not put it to the front of introduction - it disrupts the storry and it is not much relevant. Instread I put them after introduction of our simulation model, to clearly tell we simulate it on much smaller scale.
I shortened figure caption for the performance bechmakr
I wrote the text (new subsection) for the performance benchmark @NikoOinonen pleas check if what I wrote is correct.
I modified the conclusion

IMO we are almost ready to send the revision back to referees, after some proofreading. Or do you think there is something significant left?

Do you still think we should shorten the review of methods (I would prefer not do that).

@yakutovicha @mondracek please take a look on the text as well, you are much more careful about the details and languge than me and Ondrej.

ProkopHapala commented 4 months ago

I was thinking with respect to some referee comment (that there are other AFM/SPM simulation modeling softwares), that maybe it is relevant also with respect to the title.

We may change the title to

Advancing high resolution Scanning Probe Microscopy Simulations: ...

but maybe it is already too long. I don't think it is necessary. Just a thought.

NikoOinonen commented 4 months ago

I went through the text and overall it looks good to me now.

I added this note to the performance section: "It should be noted that this relationship for the execution times could be different for different types of systems, e.g.\ a non-periodic system with empty space on the sides of the simulation box can have a significantly smaller number of atoms while having a similar grid size, which would lead to the LJ+PC method being significantly faster than the other two."
@ProkopHapala In section 5.1.1 we mention the possibility of using tri-cubic interpolation instead of tri-linear which we are using now. But if I recall, you were recently saying that you did some experiments with it and the cubic interpolation is maybe not that good. Do you think we should remove this note from the paper?

ProkopHapala commented 4 months ago

@ProkopHapala In section 5.1.1 we mention the possibility of using tri-cubic interpolation instead of tri-linear which we are using now. But if I recall, you were recently saying that you did some experiments with it and the cubic interpolation is maybe not that good. Do you think we should remove this note from the paper?

I still hope tri-cubic can be useful. But is true that it is several times slower (at least my implementation) and that it require some complicated fitting with special handling of the arease of steep repulsive potential, because otherewise fit oscialtes. => I don't want to abandon it, but it is more complicated than I expected.

But I would perhaps keep the sentence.

ondrejkrejci commented 4 months ago

@ProkopHapala

Thank you a lot! @NikoOinonen as well! I am going for a 4 days holiday in Austria, and I am taking the manuscript with me, to work on it. I will be available back on Monday afternoon.

I am seeing here and there small ideas for improvement of the text, but it start a pretty good shape now.

As for the (1) - https://github.com/Probe-Particle/ppafm/issues/283 here is the issue for it. Generally speaking -- I want to show some effort, few sentences here and there. When I read about it with some distance, I can spot few places, where we are not giving that factual (extra) knowledge. I agree with you that we want to keep it as whole, but it will look better before the reviewer and the editor, that we have tried at least something.

ondrejkrejci commented 4 months ago

Completely different question - on page 3 in overleaf blue - is the equation right, or should it be a square root? @ProkopHapala

ProkopHapala commented 4 months ago

Completely different question - on page 3 in overleaf blue - is the equation right, or should it be a square root? @ProkopHapala

yes, there should be square root (I made mistake because in my FireCore code I typically do square-root beforehand for e_i and e_j separately to save time for on-the-fly mixing)

ondrejkrejci commented 4 months ago

@ProkopHapala, @NikoOinonen and @mondracek - could you please go through the intro. I think that I have updated it from my point of view, addressing the comments about not stressing novelty (in the paper and in the code - comment 1) as well as the comment 5. If this wouold be fine, than the only thing to left is comment 4 and partial shortening in 1 - (section 2 and 3 maybe). Still reading and thinking.

NikoOinonen commented 4 months ago

@ondrejkrejci Thanks, I went through it and edited some parts a little.

ProkopHapala commented 4 months ago

@ondrejkrejci I read it did some edits mostly in the part of introduction where you describe layout of sections and new developmetns.

Generally, with rescpet to the parts you want to remove (yellow), I would prefer to keep them as they makes the text more fluent and engaging and give some context. The KPFM without the equation would be very blank. I don't think this is what referee asks for (i.e. shorten the text because it is too long), referee was compainging that is looks like review paper, and that it was not clear what is new.

ondrejkrejci commented 4 months ago

@ProkopHapala - thank you for the intro, looks good to me.

Waiting for @mondracek to go through it. I will update the response afterwards. Please could you also look for the updated summary.

I will continue (a friendly) discussion about (1) and possible shortening in #283.

Except for that, I think that we are quickly converging towards something possible resubmit. Just (4) is missing at this point. @yakutovicha Will you have time later this week, or in the beginning of the next week?

Thank you all!

ProkopHapala commented 4 months ago

Except for that, I think that we are quickly converging towards something possible resubmit.

How are we with time? I remember they said "within one month" or something? Isn't it already over? I don't keep track. Anyway, I think I will not do much next week due to conference.

ondrejkrejci commented 4 months ago

How are we with time? I remember they said "within one month" or something? Isn't it already over? I don't keep track. Anyway, I think I will not do much next week due to conference.

If you feel that you can suitably address the reviewers' comments, I invite you to revise and resubmit your revised version within the next 3 months.

We are fine.

As for me - I will add my "oranges/to be removed" parts today. And we will be prepared.

ondrejkrejci commented 4 months ago

@yakutovicha - I have seen that you have went through the text. Have you removed all the oranges, that I have left there. (I am just wondering.)

ondrejkrejci commented 4 months ago

We now need to ensure this comment from the editor:

I invite you to revise and resubmit your revised version within the next 3 months. Please address carefully the issues raised in the comments and highlight in colour the changes made to the manuscript.  

If you are submitting a revised manuscript, please also:  

a) describe each change made (point by point) as raised in the reviewer comments AND/OR  

b) provide a suitable rebuttal to each reviewer comment not addressed

The only thing, that I am slightly unsure is, whether we should show, also what we have removed. But they do not say this explicitly.

aureliojgc commented 4 months ago

I believe so

El jue, 20 jun 2024, 11:48, Ondřej Krejčí @.***> escribió:

We now need to ensure this comment from the editor:

I invite you to revise and resubmit your revised version within the next 3 months. Please address carefully the issues raised in the comments and highlight in colour the changes made to the manuscript.

If you are submitting a revised manuscript, please also:

a) describe each change made (point by point) as raised in the reviewer comments AND/OR

b) provide a suitable rebuttal to each reviewer comment not addressed

The only thing, that I am slightly unsure is, whether we should show, also what we have removed. But they do not say this explicitly.

— Reply to this email directly, view it on GitHub https://github.com/Probe-Particle/ppafm/issues/68#issuecomment-2180268894, or unsubscribe https://github.com/notifications/unsubscribe-auth/AHWU4ISC4W4NDVIRK455TI3ZIKQPFAVCNFSM6AAAAAATYACMQKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCOBQGI3DQOBZGQ . You are receiving this because you were mentioned.Message ID: @.***>

ondrejkrejci commented 4 months ago

So the last 2 things that we are missing for the resubmission is the intro paragraph for a response to the editor. And action to the point "4". Otherwise it looks good to me, if it is looking good for you.

ondrejkrejci commented 2 months ago

The manuscript is published here: https://doi.org/10.1016/j.cpc.2024.109341 Once more thank you all!

Probe-Particle / ppafm

Ideas for an overview manuscript #68